# devtools::install()
# library(ContrApption)
# library(dplyr)
# #> 
# #> Attaching package: 'dplyr'
# #> The following objects are masked from 'package:stats':
# #> 
# #>     filter, lag
# #> The following objects are masked from 'package:base':
# #> 
# #>     intersect, setdiff, setequal, union
# 
# suppressMessages(library(DESeq2))
# #> Warning: package 'S4Vectors' was built under R version 3.6.3
# #> Warning: package 'GenomeInfoDb' was built under R version 3.6.3
# #> Warning: package 'DelayedArray' was built under R version 3.6.3
# suppressMessages(library(pasilla))
# 
# # loads sample annotation from the pasilla package
# pasAnno <- system.file("extdata", "pasilla_sample_annotation.csv", package = "pasilla", mustWork = TRUE)
# 
# # read in the sample data
# coldata <- read.csv(pasAnno, row.names = 1)
# 
# # select relevant columns
# coldata <- data.frame(coldata[ , c("condition","type")])
# 
# # remove un-needed characters
# rownames(coldata) <- gsub("fb", "", rownames(coldata))
# 
# # loads counts file from the pasilla package 
# pasCts <- system.file("extdata", "pasilla_gene_counts.tsv", package = "pasilla", mustWork = TRUE)
# 
# # reads counts of genes
# cts <- read.csv(pasCts, sep = "\t", row.names = "gene_id")
# 
# # make sure the order is correct
# cts <- cts[, rownames(coldata)]
# 
# # create a DESeq2 dataset from the metadata and counts
# dds <- DESeq(DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition))
# #> estimating size factors
# #> estimating dispersions
# #> gene-wise dispersion estimates
# #> mean-dispersion relationship
# #> final dispersion estimates
# #> fitting model and testing
# 
# normCounts <- counts(dds, normalized = TRUE)
# 
# res <- results(dds, tidy = TRUE) %>% 
#   data.frame %>% 
#   filter(padj < 0.05)
# 
# normCountsSig <- normCounts %>%
#   data.frame %>% 
#   filter(rownames(.) %in% res$row)
# 
# save.image("test.RData")
# # datatable(normCountsSigShared, style="bootstrap", selection = 'multiple')# devtools::install(); library(ContrApption);
load("test.RData")
library(DT)
library(crosstalk)
devtools::install()
## Skipping 2 packages not available: pasilla, DESeq2
##   
   checking for file ‘/Users/Thadryan/Dropbox (Partners HealthCare)/Workspace/RPackages/ContrApption/DESCRIPTION’ ...
  
✓  checking for file ‘/Users/Thadryan/Dropbox (Partners HealthCare)/Workspace/RPackages/ContrApption/DESCRIPTION’
## 
  
─  preparing ‘ContrApption’: (770ms)
## 
  
   checking DESCRIPTION meta-information ...
  
✓  checking DESCRIPTION meta-information
## 
  
─  checking for LF line-endings in source and make files and shell scripts (411ms)
## 
  
─  checking for empty or unneeded directories
## 
  
     NB: this package now depends on R (>= 3.5.0)
## 
  
     WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects: 'ContrApption/test.RData'
## ─  building 'ContrApption_0.0.1.9000.tar.gz'
## 
  
   
## 
Running /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL \
##   /var/folders/g0/2sgkg3j573v5c8tt_dqgkjmw0000gp/T//Rtmp0M6QxZ/ContrApption_0.0.1.9000.tar.gz \
##   --install-tests 
## * installing to library ‘/Users/Thadryan/Dropbox (Partners HealthCare)/Workspace/HFrEF_v_HFpEF_FullModel/renv/library/R-3.6/x86_64-apple-darwin15.6.0’
## * installing *source* package ‘ContrApption’ ...
## ** using staged installation
## ** R
## ** inst
## ** byte-compile and prepare package for lazy loading
## ** help
## *** installing help indices
## ** building package indices
## ** installing vignettes
## ** testing if installed package can be loaded from temporary location
## ** testing if installed package can be loaded from final location
## ** testing if installed package keeps a record of temporary installation path
## * DONE (ContrApption)
library(ContrApption)
normCountsSigShared <- SharedData$new(normCountsSig)
# ContrApption(data = normCountsSigShared, annotation = coldata)
datatable(
  normCountsSigShared, 
  style = "bootstrap",
  class = "compact",
  width = "100%",
  options = list(),
  selection = 'single'
)
ContrApption(data = normCountsSigShared, annotation = coldata)
devtools::install(); library(ContrApption); bscols(
    datatable(
    normCountsSigShared, 
    style = "bootstrap",
    class = "compact",
    width = "100%",
    options = list(),
    selection = 'single'
  ),
  ContrApption(data = normCountsSigShared, annotation = coldata)
)
## Skipping 2 packages not available: pasilla, DESeq2
##   
   checking for file ‘/Users/Thadryan/Dropbox (Partners HealthCare)/Workspace/RPackages/ContrApption/DESCRIPTION’ ...
  
✓  checking for file ‘/Users/Thadryan/Dropbox (Partners HealthCare)/Workspace/RPackages/ContrApption/DESCRIPTION’
## 
  
─  preparing ‘ContrApption’: (801ms)
## 
  
   checking DESCRIPTION meta-information ...
  
✓  checking DESCRIPTION meta-information
## 
  
─  checking for LF line-endings in source and make files and shell scripts (472ms)
## 
  
─  checking for empty or unneeded directories
## 
  
     NB: this package now depends on R (>= 3.5.0)
## 
  
     WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects: 'ContrApption/test.RData'
## ─  building 'ContrApption_0.0.1.9000.tar.gz'
## 
  
   
## 
Running /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL \
##   /var/folders/g0/2sgkg3j573v5c8tt_dqgkjmw0000gp/T//Rtmp0M6QxZ/ContrApption_0.0.1.9000.tar.gz \
##   --install-tests 
## * installing to library ‘/Users/Thadryan/Dropbox (Partners HealthCare)/Workspace/HFrEF_v_HFpEF_FullModel/renv/library/R-3.6/x86_64-apple-darwin15.6.0’
## * installing *source* package ‘ContrApption’ ...
## ** using staged installation
## ** R
## ** inst
## ** byte-compile and prepare package for lazy loading
## ** help
## *** installing help indices
## ** building package indices
## ** installing vignettes
## ** testing if installed package can be loaded from temporary location
## ** testing if installed package can be loaded from final location
## ** testing if installed package keeps a record of temporary installation path
## * DONE (ContrApption)